A key factor in the recent advances in molecular biology has been the development of reliable and convenient methods for synthesizing polynucleotides. As the use of synthetic polynucleotides has increased, the demand for greater convenience in the preparation of pure, ready-to-use polynucleotides has also increased. This demand has stimulated the development of many improvements in the basic procedures for solid phase synthesis and purification of polynucleotides. One such advance is the use of hydrophobic "handles", such as trityl moieties, in the rapid purification of synthetic oligonucleotides by reverse-phase HPLC (see, for example, Germann et al.; Ikuta et al.). This method presents advantages over ion exchange purification in that it is less time consuming and more readily scalable. The use of phosphorothioate linkages in polynucleotide analogs also reduces the resolution of ion exchange chromatography.
The RP-HPLC method can present difficulties in the purification of acid-sensitive polynucleotide analogs, however, because of the acidic conditions typically used for removal of the hydrophobic group. It would therefore be useful to have a hydrophobic purification handle that is stable to polynucleotide synthesis and ammoniolytic deprotection conditions, yet can be cleaved under mild, non-acidic conditions post purification.